5-LD Analysis Report
[Affymetrix OncoScan_CNV]
E.Bordron
2022/04/12
Microarray Information
Microarray Intensity Plot
QC Metrics
MAPD : Good < 0.20 ; Acceptable < 0.25
SNPQC : Good >= 26
WavinessSd : Good < 0.12
CNA Genomic Plots
Normalized, centered, segmented and called.
L2R + BAF
L2R
BAF
CNA Karyotypic Plot
Normalized, centered, segmented and called.
Genomic Instability Metrics Table
Segments Table
Any value (including gene symbols) can be queried in the ‘Search’ box. To search for an exact symbol try adding a coma (,) at the end of your query. Case is insensitive.
L2R
BAF
Target Genes Table
Any value can be queried in the ‘Search’ box. Case is insensitive.
Truncated Genes Table
Any value can be queried in the ‘Search’ box. Case is insensitive.
Blank cells correspond to genomic regions for which BAF is non-determined (no covering probe, thus no BAF segment).
Found 37 truncated gene(s).
CNA Chromosomal Plots
Normalized, centered, segmented and called.
chr1
chr2
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr20
chr21
chr22
chrX
chrY
Miscellaneous Information
R Session Info
## R version 4.1.2 (2021-11-01)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 17763)
##
## Matrix products: default
##
## locale:
## [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252 LC_NUMERIC=C LC_TIME=French_France.1252
##
## attached base packages:
## [1] parallel stats4 splines stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] BSgenome.Hsapiens.UCSC.hg19_1.4.3 apt.oncoscan.2.4.0_0.1.6 sequenza_3.0.0 seqinr_4.2-8
## [5] rhdf5_2.38.0 R.utils_2.11.0 R.oo_1.24.0 R.methodsS3_1.8.1
## [9] mclust_5.4.9 iotools_0.3-2 DT_0.21 dplyr_1.0.8
## [13] changepoint_2.2.2 zoo_1.8-9 BSgenome_1.62.0 rtracklayer_1.54.0
## [17] Biostrings_2.62.0 XVector_0.34.0 aroma.light_3.24.0 affxparser_1.66.0
## [21] ASCAT_3.0.0 doParallel_1.0.17 iterators_1.0.14 foreach_1.5.2
## [25] GenomicRanges_1.46.1 GenomeInfoDb_1.30.1 IRanges_2.28.0 S4Vectors_0.32.3
## [29] data.table_1.14.2 RColorBrewer_1.1-2 EaCoN_0.3.6-2 CGHbase_1.54.0
## [33] marray_1.72.0 limma_3.50.1 Biobase_2.54.0 BiocGenerics_0.40.0
##
## loaded via a namespace (and not attached):
## [1] bitops_1.0-7 matrixStats_0.61.0 bslib_0.3.1 tools_4.1.2 utf8_1.2.2
## [6] R6_2.5.1 DBI_1.1.2 rhdf5filters_1.6.0 ade4_1.7-18 tidyselect_1.1.2
## [11] compiler_4.1.2 cli_3.1.1 DelayedArray_0.20.0 sass_0.4.0 readr_2.1.2
## [16] pbapply_1.5-0 stringr_1.4.0 digest_0.6.29 Rsamtools_2.10.0 rmarkdown_2.12
## [21] pkgconfig_2.0.3 htmltools_0.5.2 MatrixGenerics_1.6.0 fastmap_1.1.0 htmlwidgets_1.5.4
## [26] rlang_1.0.1 rstudioapi_0.13 jquerylib_0.1.4 BiocIO_1.4.0 generics_0.1.2
## [31] jsonlite_1.8.0 crosstalk_1.2.0 BiocParallel_1.28.3 RCurl_1.98-1.6 magrittr_2.0.2
## [36] GenomeInfoDbData_1.2.7 Matrix_1.4-0 Rhdf5lib_1.16.0 fansi_1.0.2 lifecycle_1.0.1
## [41] stringi_1.7.6 yaml_2.3.5 oncoscanR_0.1.1 MASS_7.3-55 SummarizedExperiment_1.24.0
## [46] zlibbioc_1.40.0 grid_4.1.2 crayon_1.5.0 lattice_0.20-45 hms_1.1.1
## [51] seqminer_8.4 knitr_1.37 pillar_1.7.0 rjson_0.2.21 codetools_0.2-18
## [56] XML_3.99-0.9 glue_1.6.1 evaluate_0.15 squash_1.0.9 copynumber_1.34.0
## [61] vctrs_0.3.8 tzdb_0.2.0 purrr_0.3.4 assertthat_0.2.1 xfun_0.30
## [66] restfulr_0.0.13 tibble_3.1.6 GenomicAlignments_1.30.0 ellipsis_0.3.2